Citrus Sinensis ID: 040493

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------7
Protein Sequence
MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQADAENNEK
Secondary Structure (PSIPRED)
ccccccccccEEEEEccccEEHHHHHHHHcccccEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEEEcccccEEEEEEcEEcccccEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
mkkglhpqmQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQADAENNEK
Flexible Loop (DISEMBL)
mkkglhpqmqWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEqqadaennek
Low Complexity Region (SEG)
MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQADAENNEK
Disordered region (IsUnstruct)
********MQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQV******************
Disordered Region (DISOPRED)
******P*MQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQ*****G********************
Disordered Region (DISEMBL)
********MQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRR*************
Disordered Region (DISPRO)
****LHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQAD******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQADAENNEK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	69
255577161	68	conserved hypothetical protein [Ricinus	0.985	1.0	0.811	7e-26
224060393	68	predicted protein [Populus trichocarpa]	0.985	1.0	0.768	5e-24
77551136	143	hypothetical protein LOC_Os11g31650 [Ory	0.985	0.475	0.739	9e-24
222616045	109	hypothetical protein OsJ_34043 [Oryza sa	0.985	0.623	0.739	3e-23
215694508	68	unnamed protein product [Oryza sativa Ja	0.985	1.0	0.739	4e-23
357156679	68	PREDICTED: uncharacterized protein LOC10	0.985	1.0	0.705	4e-23
195641006	68	hypothetical protein [Zea mays] gi|41392	0.985	1.0	0.705	5e-23
116830209	77	unknown [Arabidopsis thaliana]	0.840	0.753	0.879	6e-23
186532211	76	Ribosomal protein L31 [Arabidopsis thali	0.840	0.763	0.879	6e-23
357446801	81	hypothetical protein MTR_2g014910 [Medic	0.840	0.716	0.827	1e-22

>gi|255577161|ref|XP_002529464.1| conserved hypothetical protein [Ricinus communis] gi|223531080|gb|EEF32930.1| conserved hypothetical protein [Ricinus communis]

 Score =  120 bits (302), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 56/69 (81%), Positives = 65/69 (94%), Gaps = 1/69 (1%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60
          MKKG+HPQMQWISYVTQSGRLMH+MMTKIH+VGKVYHFRARRQ+A+S+GQVAKF+RRY Q
Sbjct: 1  MKKGIHPQMQWISYVTQSGRLMHIMMTKIHHVGKVYHFRARRQLAESLGQVAKFKRRYGQ 60

Query: 61 QADAENNEK 69
          + DAE+  K
Sbjct: 61 E-DAEDTAK 68

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060393|ref|XP_002300177.1| predicted protein [Populus trichocarpa] gi|222847435|gb|EEE84982.1| predicted protein [Populus trichocarpa]

 Score =  114 bits (286), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 53/69 (76%), Positives = 63/69 (91%), Gaps = 1/69 (1%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60
          MKKG+HPQMQWISYVTQ GRLMH MMTKIH+VG VYHFRA+RQMA+S+GQ+AKF+RRY Q
Sbjct: 1  MKKGIHPQMQWISYVTQDGRLMHAMMTKIHHVGNVYHFRAKRQMAESLGQIAKFKRRYGQ 60

Query: 61 QADAENNEK 69
          + +AE+ EK
Sbjct: 61 E-NAEDAEK 68

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|77551136|gb|ABA93933.1| hypothetical protein LOC_Os11g31650 [Oryza sativa Japonica Group]

 Score =  114 bits (284), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 64/69 (92%), Gaps = 1/69 (1%)

Query: 1   MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60
           MKKGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF RRY+Q
Sbjct: 76  MKKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFNRRYQQ 135

Query: 61  QADAENNEK 69
           +++ EN EK
Sbjct: 136 ESE-ENKEK 143

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222616045|gb|EEE52177.1| hypothetical protein OsJ_34043 [Oryza sativa Japonica Group]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 64/69 (92%), Gaps = 1/69 (1%)

Query: 1   MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60
           MKKGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF RRY+Q
Sbjct: 42  MKKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFNRRYQQ 101

Query: 61  QADAENNEK 69
           +++ EN EK
Sbjct: 102 ESE-ENKEK 109

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|215694508|dbj|BAG89501.1| unnamed protein product [Oryza sativa Japonica Group] gi|215701402|dbj|BAG92826.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  112 bits (279), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 64/69 (92%), Gaps = 1/69 (1%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60
          MKKGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF RRY+Q
Sbjct: 1  MKKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFNRRYQQ 60

Query: 61 QADAENNEK 69
          +++ EN EK
Sbjct: 61 ESE-ENKEK 68

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357156679|ref|XP_003577539.1| PREDICTED: uncharacterized protein LOC100838519 isoform 2 [Brachypodium distachyon]

 Score =  111 bits (278), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 63/68 (92%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60
          M+KGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF+RRYEQ
Sbjct: 1  MRKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFKRRYEQ 60

Query: 61 QADAENNE 68
          +A+   ++
Sbjct: 61 EAEESKDK 68

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195641006|gb|ACG39971.1| hypothetical protein [Zea mays] gi|413920925|gb|AFW60857.1| hypothetical protein ZEAMMB73_243654 [Zea mays]

 Score =  111 bits (278), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 63/68 (92%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60
          M+KGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF+RRYEQ
Sbjct: 1  MRKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFKRRYEQ 60

Query: 61 QADAENNE 68
          +A+   ++
Sbjct: 61 EAEKSKDK 68

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116830209|gb|ABK28062.1| unknown [Arabidopsis thaliana]

 Score =  111 bits (277), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 51/58 (87%), Positives = 57/58 (98%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRY 58
          MKKGLHPQMQWISYVTQSGRLMHVMMT+IH+VGKVYHF A+RQMAQSIGQ+AKF+RR+
Sbjct: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTRIHHVGKVYHFGAKRQMAQSIGQIAKFKRRF 58

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186532211|ref|NP_001119440.1| Ribosomal protein L31 [Arabidopsis thaliana] gi|186532215|ref|NP_001119441.1| Ribosomal protein L31 [Arabidopsis thaliana] gi|297792983|ref|XP_002864376.1| hypothetical protein ARALYDRAFT_918652 [Arabidopsis lyrata subsp. lyrata] gi|98962143|gb|ABF59401.1| unknown protein [Arabidopsis thaliana] gi|297310211|gb|EFH40635.1| hypothetical protein ARALYDRAFT_918652 [Arabidopsis lyrata subsp. lyrata] gi|332009201|gb|AED96584.1| Ribosomal protein L31 [Arabidopsis thaliana] gi|332009202|gb|AED96585.1| Ribosomal protein L31 [Arabidopsis thaliana]

 Score =  111 bits (277), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 51/58 (87%), Positives = 57/58 (98%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRY 58
          MKKGLHPQMQWISYVTQSGRLMHVMMT+IH+VGKVYHF A+RQMAQSIGQ+AKF+RR+
Sbjct: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTRIHHVGKVYHFGAKRQMAQSIGQIAKFKRRF 58

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357446801|ref|XP_003593676.1| hypothetical protein MTR_2g014910 [Medicago truncatula] gi|355482724|gb|AES63927.1| hypothetical protein MTR_2g014910 [Medicago truncatula]

 Score =  110 bits (275), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 48/58 (82%), Positives = 56/58 (96%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRY 58
          MKKG+HPQ QWISYVTQSGRL+HVMMTKIH VGKVYHFRA+RQMA+S+GQ+AKF+RR+
Sbjct: 1  MKKGVHPQKQWISYVTQSGRLLHVMMTKIHPVGKVYHFRAKRQMAESLGQIAKFKRRF 58

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	69
TAIR|locus:4515103733	76	AT5G55125 [Arabidopsis thalian	1.0	0.907	0.805	9.4e-27

TAIR|locus:4515103733 AT5G55125 [Arabidopsis thaliana (taxid:3702)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 58/72 (80%), Positives = 67/72 (93%)

Query:     1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRY-E 59
             MKKGLHPQMQWISYVTQSGRLMHVMMT+IH+VGKVYHF A+RQMAQSIGQ+AKF+RR+ E
Sbjct:     1 MKKGLHPQMQWISYVTQSGRLMHVMMTRIHHVGKVYHFGAKRQMAQSIGQIAKFKRRFNE 60

Query:    60 QQADA--ENNEK 69
             Q+A+A  ENN +
Sbjct:    61 QEAEAAEENNNE 72


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.323   0.130   0.383    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       69        69   0.00091  102 3  11 22  0.38    28
                                                     29  0.39    29


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  509 (54 KB)
  Total size of DFA:  96 KB (2069 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  7.53u 0.10s 7.63t   Elapsed:  00:00:00
  Total cpu time:  7.53u 0.10s 7.63t   Elapsed:  00:00:00
  Start:  Fri May 10 22:03:35 2013   End:  Fri May 10 22:03:35 2013

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00012275 hypothetical protein (68 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	69
pfam01197	69	pfam01197, Ribosomal_L31, Ribosomal protein L31	5e-13

>gnl|CDD|216357 pfam01197, Ribosomal_L31, Ribosomal protein L31

 Score = 56.8 bits (138), Expect = 5e-13
 Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 10/69 (14%)

Query: 1  MKKGLHPQMQWI---------SYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQV 51
          MKKG+HP+ + +          +VT S +   V+   + +    ++   ++ +  + G+V
Sbjct: 1  MKKGIHPEYREVVFTCSSCGNVFVTGSTKEYPVIKIDVCSACHPFYTGKQK-LVDTAGRV 59

Query: 52 AKFRRRYEQ 60
           KF +R+ +
Sbjct: 60 EKFNKRFGK 68

Length = 69

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	69
TIGR00105	68	L31 ribosomal protein L31. This family consists ex	99.58
PRK00528	71	rpmE 50S ribosomal protein L31; Reviewed	99.43
PF01197	69	Ribosomal_L31: Ribosomal protein L31; InterPro: IP	99.35
PRK01678	87	rpmE2 50S ribosomal protein L31 type B; Reviewed	99.23
PRK01397	78	50S ribosomal protein L31; Provisional	99.22
PRK00019	72	rpmE 50S ribosomal protein L31; Reviewed	99.22
CHL00136	68	rpl31 ribosomal protein L31; Validated	99.21
COG0254	75	RpmE Ribosomal protein L31 [Translation, ribosomal	98.81
cd01273	142	CED-6 CED-6 Phosphotyrosine-binding (PTB) domain.	85.49
cd01274	127	AIDA-1b AIDA-1b Phosphotyrosine-binding (PTB) doma	84.16
cd01214	133	CG8312 CG8312 Phosphotyrosine-binding (PTB) domain	81.12
cd01267	132	CED6_AIDA1b Phosphotyrosine-binding (PTB) domain,	80.39

>TIGR00105 L31 ribosomal protein L31

Probab=99.58  E-value=1.2e-15  Score=93.95  Aligned_cols=58  Identities=21%  Similarity=0.427  Sum_probs=52.0

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQ   60 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~   60 (69)
                      |||||||..+.|.++.++|..+.+.+|+...  .+.         .|+|++++..+.|+|+||++||+.
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~~~ST~~~~--~i~vdi~s~~HPfyTG~~~~~~~~GRv~KF~kry~~   67 (68)
T TIGR00105         1 MKKDIHPDYHEITVTCTCGNVFTTRSTWGKE--TLNLDICSKCHPFYTGKQKIVDTGGRVDKFNKKFGG   67 (68)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEeeecCCc--eEEEEECCCCcccCCCceEEeccCCcHHHHHHHhcC
Confidence            9999999999999999999999999998543  133         799999999999999999999973

This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.

>PRK00528 rpmE 50S ribosomal protein L31; Reviewed

Probab=99.43  E-value=1.4e-13  Score=85.56  Aligned_cols=60  Identities=23%  Similarity=0.343  Sum_probs=52.1

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEe-hhhhhhHhhhhHHHHHHHhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFR-ARRQMAQSIGQVAKFRRRYEQ   60 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~-aKrqma~s~GQiAKFKRRf~~   60 (69)
                      |||||||..+-+.++.++|..+-+.+|.-.....+.         .|+ |+..+..+.|+|+||++||+.
T Consensus         1 MKk~IHP~y~~v~~~~~~g~~f~~~ST~g~~~~~i~vdv~s~~HPfyT~G~q~~~d~~GRv~kF~kky~~   70 (71)
T PRK00528          1 MKKDIHPDYHPIKVVMTDGTEYETRSTWGKTGPELRLDIDSGNHPAWTGGTQKLLDTGGRVAKFNKKFGG   70 (71)
T ss_pred             CCCCCCCCCEEEEEEEeCCCEEEEEEcCCCCCCeEEEEECCCCCccEeCCcCeEecccCcHHHHHHHHcc
Confidence            999999999999999999999999998733333333         799 999999999999999999974

>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.35  E-value=2.1e-14  Score=88.40  Aligned_cols=60  Identities=27%  Similarity=0.495  Sum_probs=48.8

Q ss_pred             CCCCccccceEEEEEee-cCeEEeeEEeEEeecceEE-------EEehhhhhhHhhhhHHHHHHHhhh
Q 040493            1 MKKGLHPQMQWISYVTQ-SGRLMHVMMTKIHNVGKVY-------HFRARRQMAQSIGQVAKFRRRYEQ   60 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq-~Grl~~vmmt~~~~~gkvy-------h~~aKrqma~s~GQiAKFKRRf~~   60 (69)
                      |||||||++++|.++.. .|..+.+.+|+....=+|=       .|+|++.+.++.|+|+||++||+.
T Consensus         1 MKk~IHP~y~~v~v~c~s~g~~~~~~St~~~~~~~vdi~s~~HPfytG~~~~~~~~Grv~KF~kkf~~   68 (69)
T PF01197_consen    1 MKKGIHPEYREVKVTCSSCGNTFETRSTKEYPVIKVDICSNCHPFYTGKQKVVDTAGRVEKFNKKFGK   68 (69)
T ss_dssp             --SSTSSSHCEEEEEES-SSSCECECSSSSES-EEECSCSSSSCTTCSCSSCSCCCCCCTSCCTCCCC
T ss_pred             CCCCCCCCCEEEEEEEcCCCCEEEEEECCcceEEEEeecCCCCEEEcCcEEEEccccCHHHHHHHHcC
Confidence            89999999999999988 8999999999832211111       799999999999999999999974

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....

>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed

Probab=99.23  E-value=7.3e-12  Score=81.36  Aligned_cols=63  Identities=27%  Similarity=0.496  Sum_probs=54.4

Q ss_pred             CCCCccccceEEEEE-eecCeEEeeEEeEEeec------ceE---E----------EEehhhhhhHhhhhHHHHHHHhhh
Q 040493            1 MKKGLHPQMQWISYV-TQSGRLMHVMMTKIHNV------GKV---Y----------HFRARRQMAQSIGQVAKFRRRYEQ   60 (69)
Q Consensus         1 mkKGlHPqmq~Is~V-tq~Grl~~vmmt~~~~~------gkv---y----------h~~aKrqma~s~GQiAKFKRRf~~   60 (69)
                      |||||||..+-|.++ .+.|..+.+.+|+....      |+-   +          -|+|+.....+.|+|+||++||+.
T Consensus         1 MKk~IHP~y~~v~~~~~t~g~~f~~~ST~~~~~t~~~~dg~~yp~i~vdi~S~~HPFyTGkq~~vdt~GRVekF~kry~~   80 (87)
T PRK01678          1 MKKGIHPEYRPVVFHDTSTGFKFLTGSTITTDETIEWEDGKTYPLVKVEISSASHPFYTGKQKFVDTEGRVEKFNKRFGR   80 (87)
T ss_pred             CCCCCCCCCEEEEEEECCCCCEEEEeeeccccceeeecCCcccceEEEEeCCCCCCcCcCCeeEeccCCcHHHHHHHHhh
Confidence            999999999999999 68999999999986432      442   2          799999999999999999999997


Q ss_pred             hhh
Q 040493           61 QAD   63 (69)
Q Consensus        61 ~~~   63 (69)
                      ...
T Consensus        81 ~~~   83 (87)
T PRK01678         81 FAS   83 (87)
T ss_pred             hhh
Confidence            754

>PRK01397 50S ribosomal protein L31; Provisional

Probab=99.22  E-value=1.1e-11  Score=79.07  Aligned_cols=59  Identities=22%  Similarity=0.409  Sum_probs=49.0

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhh-h-hHhhhhHHHHHHHhhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQ-M-AQSIGQVAKFRRRYEQQA   62 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrq-m-a~s~GQiAKFKRRf~~~~   62 (69)
                      |||||||..+-|.+.. +|..+.+.+|+..  ..+.         -|+|+.+ + ..+.|+|+||++||+.+.
T Consensus         1 MKk~IHP~y~~v~~~~-~G~~f~~~ST~~~--~~i~vdi~s~~HPFyTG~q~~~vdt~~GRVeKF~kry~~~~   70 (78)
T PRK01397          1 MKSGIHPEYKKFLIKV-GSDVFETMSTHPT--GEILMDVDFRKHPAWNKDSGNVVNQSNKSVSDFNKRFSGLS   70 (78)
T ss_pred             CCCCCCCCCEEEEEEE-CCCEEEEeECCCC--CcEEEEeCCCCCCcCcCCeeEEecCCCccHHHHHHHHcCcc
Confidence            9999999999999886 8999999999842  2233         7999965 3 456899999999999884

>PRK00019 rpmE 50S ribosomal protein L31; Reviewed

Probab=99.22  E-value=1.2e-11  Score=77.73  Aligned_cols=59  Identities=19%  Similarity=0.487  Sum_probs=51.7

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQQ   61 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~~   61 (69)
                      |||||||..+-|.++-..|..|.+.+|....  .+.         -|+|++.+..+.|+|+||++||+..
T Consensus         1 MKk~IHP~y~~v~~~c~~g~~f~~~ST~~~~--~i~vdi~s~~HPFyTG~q~~~dt~GRvekF~kry~~~   68 (72)
T PRK00019          1 MKKDIHPKYEEVTVTCSCGNVFETRSTLGKD--EINVDVCSKCHPFYTGKQKIVDTGGRVERFNKRFGKK   68 (72)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEeecCCCC--cEEEEeCCCCCCcCcCCEeEeccCCcHHHHHHHhccc
Confidence            9999999999999999999999999995322  233         7999999999999999999999865

>CHL00136 rpl31 ribosomal protein L31; Validated

Probab=99.21  E-value=1.1e-11  Score=77.13  Aligned_cols=55  Identities=29%  Similarity=0.443  Sum_probs=45.3

Q ss_pred             CCCCccccceEEEEEeecCeE-EeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRL-MHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYE   59 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl-~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~   59 (69)
                      |||||||..+.+..|+-+|.. +.+-+|+    +.+.         .|+|++.+..+.|+|+||++||+
T Consensus         2 MKk~IHP~y~~~~~v~c~~~~~~~~~ST~----~~i~vdv~s~~HPfyTG~~~~~~~~Grv~kF~kr~~   66 (68)
T CHL00136          2 PKKNIHPQWFPETKVYCDGQLVMTVGSTK----PELNVDIWSGNHPFYTGSQKIIDTEGRVERFMKKYG   66 (68)
T ss_pred             CCCCCCCCceeeEEEEEcCCCEEEEeecC----CCEEEEeCCCCCccCcCCeeEecccccHHHHHHHhC
Confidence            899999999877666666666 7776665    3343         79999999999999999999997

>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]

Probab=98.81  E-value=4.2e-09  Score=67.33  Aligned_cols=63  Identities=22%  Similarity=0.332  Sum_probs=49.6

Q ss_pred             CCCCccccceEEEEEeec--CeEEeeEEeEEeecceEE-------EEehhhhhhHhhhhHHHHHHHhhhhhh
Q 040493            1 MKKGLHPQMQWISYVTQS--GRLMHVMMTKIHNVGKVY-------HFRARRQMAQSIGQVAKFRRRYEQQAD   63 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~--Grl~~vmmt~~~~~gkvy-------h~~aKrqma~s~GQiAKFKRRf~~~~~   63 (69)
                      |||||||-.+..-++..+  |-.|-+.+|+....=.|=       -|+|+.....+-|.|+||++||+....
T Consensus         1 MKk~IHP~y~~~v~~~~~s~g~~f~~~ST~~~~~i~vdV~s~~HPFyTG~qk~~d~~Grv~kF~kRf~~~~~   72 (75)
T COG0254           1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTDEINLDVCSKCHPFYTGKQKIVDTEGRVEKFNKRFGGFKG   72 (75)
T ss_pred             CCCCcCCCccceEEEEeCCCCCEEEEEeccCCceEEEEeCCCCCCcCcCceeEeeccccHHHHHHHhccccc
Confidence            999999998665555554  999999999965521111       699999988888999999999987643

>cd01273 CED-6 CED-6 Phosphotyrosine-binding (PTB) domain

Probab=85.49  E-value=3.6  Score=27.37  Aligned_cols=50  Identities=20%  Similarity=0.323  Sum_probs=33.3

Q ss_pred             ceEEEEEeecCeEEeeEEeEEeec---ceEE--EEehhh---hhhHhhhhHHHHHHHhhh
Q 040493            9 MQWISYVTQSGRLMHVMMTKIHNV---GKVY--HFRARR---QMAQSIGQVAKFRRRYEQ   60 (69)
Q Consensus         9 mq~Is~Vtq~Grl~~vmmt~~~~~---gkvy--h~~aKr---qma~s~GQiAKFKRRf~~   60 (69)
                      +++|||++.+...-+++.=.-.+.   ++.+  .|..+.   .++.++||.  |...|+.
T Consensus        82 i~~ISfca~d~~~~r~FayIak~~~~~~~~~ChvF~s~~~A~~I~~tigqA--F~~ay~~  139 (142)
T cd01273          82 LGRISFCADDKDDKRMFSFIAKAEGASGKHSCFVFTSEKLAEDITLTIGQA--FDLAYRK  139 (142)
T ss_pred             cceEEEEecCCCCCeEEEEEecCCCCCCcEEEEEEeccchHHHHHHHHHHH--HHHHHHH
Confidence            789999999988777666554443   3333  444433   466788986  7777764

CED-6 Phosphotyrosine-binding (PTB) domain. CED6 is an adaptor protein involved in the engulfment of apoptotic cells. It has a C-terminal PTB domain, which can bind to NPXY motifs. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.

>cd01274 AIDA-1b AIDA-1b Phosphotyrosine-binding (PTB) domain

Probab=84.16  E-value=4.5  Score=26.92  Aligned_cols=52  Identities=19%  Similarity=0.317  Sum_probs=32.9

Q ss_pred             cccceEEEEEeecCeEEeeEEeEEeecc-eEE--EEeh-h----hhhhHhhhhHHHHHHHhhh
Q 040493            6 HPQMQWISYVTQSGRLMHVMMTKIHNVG-KVY--HFRA-R----RQMAQSIGQVAKFRRRYEQ   60 (69)
Q Consensus         6 HPqmq~Is~Vtq~Grl~~vmmt~~~~~g-kvy--h~~a-K----rqma~s~GQiAKFKRRf~~   60 (69)
                      || |++|||++++..--+++.-.-.+.+ ..+  -|.. +    ..+..++||+  |+.+|+.
T Consensus        66 ~~-i~~ISf~~~D~~d~~~FayIakd~~~~~~CHvF~~~~~~~A~~I~~tigqA--F~~ay~~  125 (127)
T cd01274          66 HG-IYNIRCVCQDREDLNFFAYITKDTENRHYCHVFCVLTSGLAAEIITTLGQA--FEVAYQL  125 (127)
T ss_pred             ee-eeEEEEEecCCCCceEEEEEeeCCCCCEEEEEEEcCCHHHHHHHHHHHHHH--HHHHHhh
Confidence            44 6999999988876555544433333 333  4442 2    4566788986  7777764

AIDA-1b Phosphotyrosine-binding (PTB) domain. AIDA-1b is an amyloid-beta precursor protein interacting protein. It consists of ankyrin repeats, a SAM domain and a C-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.

>cd01214 CG8312 CG8312 Phosphotyrosine-binding (PTB) domain

Probab=81.12  E-value=2.6  Score=29.28  Aligned_cols=42  Identities=21%  Similarity=0.228  Sum_probs=32.8

Q ss_pred             cceEEEEEeecCeEEeeEEeEEeecceE-----E---EEehhhhhhHhhh
Q 040493            8 QMQWISYVTQSGRLMHVMMTKIHNVGKV-----Y---HFRARRQMAQSIG   49 (69)
Q Consensus         8 qmq~Is~Vtq~Grl~~vmmt~~~~~gkv-----y---h~~aKrqma~s~G   49 (69)
                      .++||||.+.+-+.=+|+.-+-.+.++-     .   -+-.|+++|+++-
T Consensus        66 ~i~RIsYCsad~~~p~VFa~I~r~~~~~~~~~l~CHAvlC~k~~~A~aia  115 (133)
T cd01214          66 WAHRITYCVAPARYPKVFCWIYRHEGKHLKVELRCHAVLCSKPEKAQAIA  115 (133)
T ss_pred             EEeeeeeecCCcCCCcEEEEEEeecccccCcceEEEEEEeCCHHHHHHHH
Confidence            4699999999999888888777777652     2   4678888888754

CG8312 Phosphotyrosine-binding (PTB) domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.

>cd01267 CED6_AIDA1b Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain

Probab=80.39  E-value=8.9  Score=24.72  Aligned_cols=50  Identities=22%  Similarity=0.311  Sum_probs=29.7

Q ss_pred             ceEEEEEeecCeEEeeEEeEEeec--ceEE--EEehh-----hhhhHhhhhHHHHHHHhhh
Q 040493            9 MQWISYVTQSGRLMHVMMTKIHNV--GKVY--HFRAR-----RQMAQSIGQVAKFRRRYEQ   60 (69)
Q Consensus         9 mq~Is~Vtq~Grl~~vmmt~~~~~--gkvy--h~~aK-----rqma~s~GQiAKFKRRf~~   60 (69)
                      +++|||++.+..--+++.=+-...  ++.+  -|...     ..+..++||.  |+.+|..
T Consensus        72 i~~ISfc~~d~~~~~~FafIa~~~~~~~~~ChvF~~~~~~~A~~I~~tig~A--F~~ay~~  130 (132)
T cd01267          72 LYNISCCAQDKEDLRFFAFIAKDTETNKHYCHVFCSEKLGLAEEIILTIGQA--FELAYRL  130 (132)
T ss_pred             cceEEEEecCCCCCeEEEEEEecCCCCceEEEEEECCCHHHHHHHHHHHHHH--HHHHHHh
Confidence            689999998765444443332322  2433  34433     3567788886  7777753

Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	69
1nkw_Y	73	50S ribosomal protein L31; ribosome, large subunit	99.39
1vs6_Z	70	50S ribosomal protein L31; ribosome, kasugamycin;	99.28
3v2d_4	71	50S ribosomal protein L31; ribosome associated inh	99.04
3f1f_4	97	50S ribosomal protein L31; RF2, ribosome, terminat	98.79
3bbo_1	144	Ribosomal protein L31; large ribosomal subunit, sp	98.01
1ntv_A	152	Disabled homolog 1; beta-sandwich, signaling prote	86.48
4dbb_A	162	Amyloid beta A4 precursor protein-binding family 1	82.71
2ela_A	175	Adapter protein containing PH domain, PTB domain a	82.55
2ej8_A	160	DCC-interacting protein 13 alpha; structural genom	80.99

>1nkw_Y 50S ribosomal protein L31; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_Y* 1nwy_Y* 1pnu_Y 1pny_Y 1sm1_Y* 1vor_1 1vou_1 1vow_1 1voy_1 1vp0_1 1xbp_Y* 1yl3_4 2b66_4 2b9n_4 2b9p_4

Probab=99.39  E-value=1.3e-13  Score=86.17  Aligned_cols=61  Identities=23%  Similarity=0.388  Sum_probs=54.9

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhhhhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQQADAE   65 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~~~~ae   65 (69)
                      |||||||..+.|.++-+.|..+.+.+|...    +.         -|+|+..+..+.|+|+||++||+....+.
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~t~ST~~~----i~vdi~s~~HPFyTGkqk~vdt~GRVekF~kry~~~~~~~   70 (73)
T 1nkw_Y            1 MQKDLHPKAVPCKIIYQGQVVMETMSTRPE----IHVDVWSGVHPFWTGEERFLDTEGRVDKFNKRFGDSYRRG   70 (73)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEcccCCC----EEEEECCCCCcCCcCcEEEEeccccHHHHHHHHhcccccc
Confidence            999999999999999999999999999863    32         68999999999999999999999877643

>1vs6_Z 50S ribosomal protein L31; ribosome, kasugamycin; 3.46A {Escherichia coli} SCOP: d.325.1.2 PDB: 1vs8_Z 2aw4_Z 2awb_Z 2j28_Z 2rdo_Z 2vhm_Z 2vhn_Z 3bbx_Z 3e1b_S 3e1d_S 3iyx_A 3iyy_A 3izt_b* 3izu_b* 3j0t_2* 3j0w_2* 3j0y_2* 3j11_2* 3j12_2* 3j14_2*

Probab=99.28  E-value=5.4e-14  Score=87.06  Aligned_cols=61  Identities=25%  Similarity=0.437  Sum_probs=52.6

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEe-------ecceEEEEehhhhhhHhhhhHHHHHHHhhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIH-------NVGKVYHFRARRQMAQSIGQVAKFRRRYEQQA   62 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~-------~~gkvyh~~aKrqma~s~GQiAKFKRRf~~~~   62 (69)
                      |||||||..+.|.++-+.|..+.+.+|...       ...-- -|+|+..+..+.|+|+||++||+...
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~t~ST~~~ei~vdi~s~~HP-FyTG~qk~vdt~GRV~kF~kry~~~~   68 (70)
T 1vs6_Z            1 MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHP-FFTGKQRDVATGGRVDRFNKRFNIPG   68 (70)
T ss_dssp             CCCTTSCCCCCCBCCCCSSCCCCCBCCCCCCCCCBCCSSSCC-BCCCCCTTTTTHHHHSCSSTTTTTTS
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEeecCCCcEeeeecCCCCc-cCcCcEEEEeccccHHHHHHHhhccc
Confidence            999999999999999999999999999753       11122 59999999999999999999998753

>3v2d_4 50S ribosomal protein L31; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_3 2hgj_3 2hgu_3 2j03_4 2v47_4 2v49_4 2wdi_4 2wdj_4 2wdl_4 2wdn_4 2wh2_4 2wrj_4 2wrl_4 2wro_4 2wrr_4 2x9s_4 2x9u_4 2xg0_4 2xg2_4 2xqe_4 ...

Probab=99.04  E-value=9e-11  Score=73.17  Aligned_cols=57  Identities=26%  Similarity=0.621  Sum_probs=32.7

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQQ   61 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~~   61 (69)
                      |||||||..+-|.++-+.|..|.+-+|+.    .+.         -|+|+..+..+.|+|+||++||+..
T Consensus         1 MKk~IHP~Y~~v~v~c~~g~~f~t~ST~~----~i~vdi~S~~HPFyTGkqk~vdt~GRVekF~kryg~~   66 (71)
T 3v2d_4            1 MKEGIHPKLVPARIICGCGNVIETYSTKP----EIYVEVCSKCHPFYTGQQRFVDTEGRVERFQRRYGDS   66 (71)
T ss_dssp             CCSSSSCCCEEEEEEETTSCEEEEEESSS----EEEESCCTTTSSSSSCC--------------------
T ss_pred             CCCCCCCCCeEEEEEECCCCEEEeeeecc----CEEEEecCCCCCCCCCCEEEEcccCcHHHHHHHHccc
Confidence            99999999999999989999999999975    244         5999999999999999999999754

>3f1f_4 50S ribosomal protein L31; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 3d5d_4 3d5b_4 3f1h_4

Probab=98.79  E-value=6.6e-10  Score=73.00  Aligned_cols=57  Identities=25%  Similarity=0.605  Sum_probs=19.0

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQQ   61 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~~   61 (69)
                      |||||||..+-|.++-+.|..|.+-+|+.    .+.         -|+|+..+..+.|+|+||++||...
T Consensus        27 MKk~IHP~Y~~v~v~ct~G~~f~t~ST~~----~i~vDI~S~~HPFYTGkqk~vdt~GRVeKF~kRyg~~   92 (97)
T 3f1f_4           27 VKEGIHPKLVPARIICGCGNVIETYSTKP----EIYVEVCSKCHPFYTGQQRFVDTEGRVERFQRRYGDS   92 (97)
T ss_dssp             ---------CCCEEEETTEEEEECCCSSC----CEEESSCTTC---------------------------
T ss_pred             ccCCCCCCCeEEEEEECCCCEEEeeeeee----EEEEEECCCCCCCCcCCEEEEcccCcHHHHHHHHccc
Confidence            89999999999999989999999999974    233         5999999999999999999999753

>3bbo_1 Ribosomal protein L31; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=98.01  E-value=3.5e-09  Score=73.64  Aligned_cols=61  Identities=28%  Similarity=0.354  Sum_probs=44.7

Q ss_pred             CCCCccccceEEEEEeecCeEEe-eEEeEEeecceEE---------EEehhhh-hhHhhhhHHHHHHHhhhhhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMH-VMMTKIHNVGKVY---------HFRARRQ-MAQSIGQVAKFRRRYEQQADAE   65 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~-vmmt~~~~~gkvy---------h~~aKrq-ma~s~GQiAKFKRRf~~~~~ae   65 (69)
                      ||+||||..+-+.+|..+|..+- +-+|..    .+.         -|+|+.+ +..+.|+|+||++||+..++++
T Consensus        49 MKk~IHPeY~~Vv~v~cs~g~~f~t~ST~~----~i~VDIcS~cHPFYTGkqkk~vDt~GRVeKF~KRyg~~~~~~  120 (144)
T 3bbo_1           49 RKKELHPEFHEDAKVYCNGELVMTTGGTKK----EYVVDVWSGNHPFYLGNRSALMVDADQVEKFRKRFAGLSEIM  120 (144)
T ss_dssp             -CTTTCCCCCHHHHHCSSSCTTTSCSSCSC----SSSCCSSCCCCCSSSSSSSCCCCCCCCCCCSSCCCCCCSSCC
T ss_pred             cCCCCCCCCEEeEEEEcCCCeEEEEEecCc----eEEeeecCCCCccEeCceeeEecccccHHHHHHHHhcccccc
Confidence            89999999887677777766544 444432    122         6999876 7888999999999998776643

>1ntv_A Disabled homolog 1; beta-sandwich, signaling protein; 1.50A {Mus musculus} SCOP: b.55.1.2 PDB: 1nu2_A* 1oqn_A*

Probab=86.48  E-value=0.63  Score=29.99  Aligned_cols=53  Identities=11%  Similarity=0.149  Sum_probs=33.4

Q ss_pred             ceEEEEEeecCeEEeeEEeEEee-cceEEE-Eehh---hhhhHhhhhHHHHHHHhhhhhh
Q 040493            9 MQWISYVTQSGRLMHVMMTKIHN-VGKVYH-FRAR---RQMAQSIGQVAKFRRRYEQQAD   63 (69)
Q Consensus         9 mq~Is~Vtq~Grl~~vmmt~~~~-~gkvyh-~~aK---rqma~s~GQiAKFKRRf~~~~~   63 (69)
                      |++|||++++.+--+++.-.-.+ ...+|+ +...   ..+..++||.  |...|++...
T Consensus        88 l~~ISf~a~d~~d~r~FafI~k~~~~h~f~v~~s~~~A~~I~~tigqA--F~~ay~~~~~  145 (152)
T 1ntv_A           88 VHEISYIAKDITDHRAFGYVCGKEGNHRFVAIKTAQAAEPVILDLRDL--FQLIYELKQR  145 (152)
T ss_dssp             GGGEEEEEECTTCTTEEEEEESSTTCCEEEEEEESSCSHHHHHHHHHH--HHHHHHHHHT
T ss_pred             cCcEEEEeCCCCCCcEEEEEEEcCCeEEEEEEccHHHHHHHHHHHHHH--HHHHHHHHhH
Confidence            58999999987664444333222 223443 3333   6788899996  7777776655

>4dbb_A Amyloid beta A4 precursor protein-binding family 1; X11S/mints, PTB domain, chimera protein, protein transport; HET: IPA GOL; 1.90A {Rattus norvegicus}

Probab=82.71  E-value=2.9  Score=27.22  Aligned_cols=51  Identities=27%  Similarity=0.485  Sum_probs=31.2

Q ss_pred             ceEEEEEeecCeEEeeEEeEE------eecceEEEEehhhhhhHhhhhHHHHHHHhhhh
Q 040493            9 MQWISYVTQSGRLMHVMMTKI------HNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQ   61 (69)
Q Consensus         9 mq~Is~Vtq~Grl~~vmmt~~------~~~gkvyh~~aKrqma~s~GQiAKFKRRf~~~   61 (69)
                      |++|||++++++.+-.+.-..      .+.=.||.=..-..++.++||.  |.-+|..-
T Consensus        80 l~~ISf~a~~~~~f~fIar~~~~~~~~~~~CHVF~~~~A~~I~~tigqA--F~~ay~~~  136 (162)
T 4dbb_A           80 LRTISYIADIGNIVVLMARRRMPRSQYKMICHVFESEDAQLIAQSIGQA--FSVAYQEF  136 (162)
T ss_dssp             GGGEEEEEEETTEEEEEEEECCSTTCEEEEEEEEECTTHHHHHHHHHHH--HHHHHGGG
T ss_pred             cceeEEEEECCCEEEEEeccCCCCCCCcEEEEEEECCCHHHHHHHHHHH--HHHHHHHH
Confidence            689999999887665544332      1112233222245678889986  77777543

>2ela_A Adapter protein containing PH domain, PTB domain and leucine zipper motif 1; APPL, cell cycle; 2.00A {Homo sapiens}

Probab=82.55  E-value=4.3  Score=26.94  Aligned_cols=56  Identities=9%  Similarity=0.138  Sum_probs=32.3

Q ss_pred             ceEEEEEeecCeEEeeEEeEEeec-------ceE--EEEehh---hhhhHhhhhHHHHHHHhhhhhhhhh
Q 040493            9 MQWISYVTQSGRLMHVMMTKIHNV-------GKV--YHFRAR---RQMAQSIGQVAKFRRRYEQQADAEN   66 (69)
Q Consensus         9 mq~Is~Vtq~Grl~~vmmt~~~~~-------gkv--yh~~aK---rqma~s~GQiAKFKRRf~~~~~ae~   66 (69)
                      ++.|||++++...-+++.=+-...       ...  |-|...   ..++.++||.  |..+|+..-+++.
T Consensus        97 i~~ISfca~d~~d~r~FafIar~~~~~~~~~~~~~CHVF~~~~~A~~I~~tIgqA--F~~ay~~~l~~~~  164 (175)
T 2ela_A           97 LPCVVLYATHQENKRLFGFVLRTSSGRSESNLSSVCYIFESNNEGEKICDSVGLA--KQIALHAELDRRA  164 (175)
T ss_dssp             GGGEEEEEEETTEEEEEEEEEEEC-------CEEEEEEEEESSCHHHHHHHHHHH--HHHHHHHHHCC--
T ss_pred             cCEEEEEEeCCCCCcEEEEEEecCccccCCCcceEEEEEEcchhHHHHHHHHHHH--HHHHHHHHHHhhH
Confidence            589999999987544443332222       111  233332   3467788986  8888876555333

>2ej8_A DCC-interacting protein 13 alpha; structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.84A {Homo sapiens}

Probab=80.99  E-value=5.6  Score=25.68  Aligned_cols=55  Identities=9%  Similarity=0.149  Sum_probs=30.5

Q ss_pred             ceEEEEEeecCeEEeeEEeEEeec-------ce--EEEEehh---hhhhHhhhhHHHHHHHhhhhhhhh
Q 040493            9 MQWISYVTQSGRLMHVMMTKIHNV-------GK--VYHFRAR---RQMAQSIGQVAKFRRRYEQQADAE   65 (69)
Q Consensus         9 mq~Is~Vtq~Grl~~vmmt~~~~~-------gk--vyh~~aK---rqma~s~GQiAKFKRRf~~~~~ae   65 (69)
                      ++.|||++++...-+++.=+-.+.       ..  -|-|...   ..++.++||.  |...|+..-+++
T Consensus        84 i~~ISfca~d~~~~r~FafIar~~~~~~~~~~~~~CHVF~~~~~A~~I~~tigqA--F~~ay~~~l~~~  150 (160)
T 2ej8_A           84 LPCVVLYATHQENKRLFGFVLRTSSGRSESNLSSVCYIFESNNEGEKICDSVGLA--KQIALHAELDRR  150 (160)
T ss_dssp             GGGEEEEEEETTEEEEEEEEEEECC------CEEEEEEEEESSCHHHHHHHHHHH--HHHHHHHC----
T ss_pred             CCeEEEEEecCCCCeEEEEEEecCCcccCCCccEEEEEEEcchhHHHHHHHHHHH--HHHHHHHHHHHh
Confidence            688999999987544443332222       11  1233332   3466788986  777787655533

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	69
d1vs6z1	70	d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escheri	1e-04

>d1vs6z1 d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia coli [TaxId: 562]} Length = 70

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Escherichia coli [TaxId: 562]

 Score = 33.9 bits (78), Expect = 1e-04
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 14/68 (20%)

Query: 1  MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYH----------FRARRQMAQSIGQ 50
          MKK +HP+ + I+     G +M +  T    VG   +          F  +++   + G+
Sbjct: 1  MKKDIHPKYEEITASCSCGNVMKIRST----VGHDLNLDVCSKCHPFFTGKQRDVATGGR 56

Query: 51 VAKFRRRY 58
          V +F +R+
Sbjct: 57 VDRFNKRF 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	69
d1vs6z1	70	Ribosomal protein L31p {Escherichia coli [TaxId: 5	99.12
d2j0141	50	Ribosomal protein L31p {Thermus thermophilus [TaxI	94.48

>d1vs6z1 d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Escherichia coli [TaxId: 562]

Probab=99.12  E-value=4.5e-13  Score=81.18  Aligned_cols=59  Identities=25%  Similarity=0.488  Sum_probs=52.0

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhhhh
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQQA   62 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~~~   62 (69)
                      |||||||..+-+.++.++|..+.+.+|....   +.         -|+|+..+..+.|+|+||++||+..+
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~~~sT~~~e---~~vdi~s~~HPfyTG~q~~~dt~GRVekF~krf~~~~   68 (70)
T d1vs6z1           1 MKKDIHPKYEEITASCSCGNVMKIRSTVGHD---LNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIPG   68 (70)
T ss_dssp             CCCTTSCCCCCCBCCCCSSCCCCCBCCCCCC---CCCBCCSSSCCBCCCCCTTTTTHHHHSCSSTTTTTTS
T ss_pred             CCCCCCCCCEeEEEEECCCCEEEEeeEeCCc---EEEEeCCCCCCcCcCCEEEeeccCcHHHHHHhhcccc
Confidence            9999999999999999999999999986321   22         79999999999999999999998754

>d2j0141 d.325.1.2 (4:1-50) Ribosomal protein L31p {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Thermus thermophilus [TaxId: 274]

Probab=94.48  E-value=0.00023  Score=40.16  Aligned_cols=28  Identities=29%  Similarity=0.539  Sum_probs=23.9

Q ss_pred             CCCCccccceEEEEEeecCeEEeeEEeE
Q 040493            1 MKKGLHPQMQWISYVTQSGRLMHVMMTK   28 (69)
Q Consensus         1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~   28 (69)
                      |||||||..+-+.+.-..|..|.+.+|+
T Consensus         1 MKk~IHP~y~~v~~~cscg~~f~~~ST~   28 (50)
T d2j0141           1 MKEGIHPKLVPARIICGCGNVIETYSTK   28 (50)
T ss_dssp             CCGGGCCCCTTTTTCTTSCGGGSCSSSS
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEecccC
Confidence            9999999998888777778888877775